Problem exporting in avogado 1.93.0 (kubuntu20.4) for research

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1

hello,

i use avogadro for research and up to now loved its simplicity and efficiency.
since i had to upgrade my linux to 20.4, avogadro 1.93 can simply just not export any type of suitable molecule. i am particularly interested in the pdb format, which is universal for research and generating new compounds coordinated for refinements and modelling.
I read that the pdb format support has been deprecated. i find this disturbing due to its ubiquitous use. Are there plans to get the pdb support in avogadro or alternatives? pdbq export format also does not work in my setup for some reason.

cheers,
Max

2

Yes, it’s a bug - something in the logic with the export window.

It’s not that PDB has been deprecated. It’s that we want to be clear that saving to PDB, XYZ, etc. can involve loss of data. (For example, many people are surprised when they save to PDB or particularly XYZ and read back and bonds may not remain identical.)

Let me see if I can take a crack at the fix.